Kids Book Recommendations

So I have a nephew who is about to turn 7. This kid is WICKED smart. However, his mom (my sister) is getting very evangelical with me, and there are some things he's said that really concern me. Just a bit of back story for a snap shot:

At Christmas, my sister wanted to know why I had strayed from the faith. I explained it logically, and how I don't begrudge anyone who has come to different answers because they've been on a different path. "It's just where I am". She then knowingly said "Oh. Just where you are." Like "ah, whew. It's just a phase."

This kid has ALWAYS loved dinosaurs. He's wanted to be a paleontologist since before he could really pronounce it. So I was talking to him about all the different animals, and what they turned into, and evolution. As soon as I said the E word, he said "Well, that's just a theory. No one REALLY knows what happened." It utterly floored me. That's not something he came up with on his own - it's something he's been told, and he's internalizing as fact.

I was talking about books with his mom. I talked about how much I ADORED Roald Dahl when I was a kid. My favorite was Matilda. When I told her it's about an overly bright girl who helps her sweet teacher overcome the mean bullying principal, she was totally turned off. She said "I'm not quite ready to introduce him to the idea of authority figures who can't be trusted." BWUHH???? She's let this kid read every Harry Potter book - what do you call Snape? Regardless, the kind of "tip toe" approach to the real world really bothered me.

So, while I'd never have thought do be so passive aggressive, her comments about shielding him from the reality of the world makes me want to buy him a subtly subversive book for his birthday.

What's a good kid's book that isn't overtly atheist, but teaches him a bit about thinking on his own, and encourages a bit of good natured rebellion?